Subset: Sequencing
URI: Sequencing
Slots in subset
| Slot | Description |
|---|---|
| adapters | Adapters provide priming sequences for both amplification and sequencing of t... |
| annot | Tool used for annotation, or for cases where annotation was provided by a com... |
| assembly_name | Name/version of the assembly provided by the submitter that is used in the ge... |
| assembly_qual | The assembly quality category is based on sets of criteria outlined for each ... |
| assembly_software | Tool(s) used for assembly, including version number and parameters |
| associated_resource | A related resource that is referenced, cited, or otherwise associated to the ... |
| bin_param | The parameters that have been applied during the extraction of genomes from m... |
| bin_software | Tool(s) used for the extraction of genomes from metagenomic datasets, where p... |
| chimera_check | Tool(s) used for chimera checking, including version number and parameters, t... |
| compl_appr | The approach used to determine the completeness of a given genomic assembly, ... |
| compl_score | Completeness score is typically based on either the fraction of markers found... |
| compl_software | Tools used for completion estimate, i |
| contam_score | The contamination score is based on the fraction of single-copy genes that ar... |
| contam_screen_input | The type of sequence data used as input |
| contam_screen_param | Specific parameters used in the decontamination sofware, such as reference da... |
| decontam_software | Tool(s) used in contamination screening |
| detec_type | Type of UViG detection |
| feat_pred | Method used to predict UViGs features such as ORFs, integration site, etc |
| host_pred_appr | Tool or approach used for host prediction |
| host_pred_est_acc | For each tool or approach used for host prediction, estimated false discovery... |
| lib_layout | Specify whether to expect single, paired, or other configuration of reads |
| lib_reads_seqd | Total number of clones sequenced from the library |
| lib_screen | Specific enrichment or screening methods applied before and/or after creating... |
| lib_size | Total number of clones in the library prepared for the project |
| lib_vector | Cloning vector type(s) used in construction of libraries |
| mag_cov_software | Tool(s) used to determine the genome coverage if coverage is used as a binnin... |
| mid | Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... |
| nucl_acid_amp | A link to a literature reference, electronic resource or a standard operating... |
| nucl_acid_ext | A link to a literature reference, electronic resource or a standard operating... |
| number_contig | Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| otu_class_appr | Cutoffs and approach used when clustering species-level OTUs |
| otu_db | Reference database (i |
| otu_seq_comp_appr | Tool and thresholds used to compare sequences when computing "species-level" ... |
| pcr_cond | Description of reaction conditions and components of polymerase chain reactio... |
| pcr_primers | PCR primers that were used to amplify the sequence of the targeted gene, locu... |
| pred_genome_struc | Expected structure of the viral genome |
| pred_genome_type | Type of genome predicted for the UViG |
| reassembly_bin | Has an assembly been performed on a genome bin extracted from a metagenomic a... |
| ref_db | List of database(s) used for ORF annotation, along with version number and re... |
| sc_lysis_approach | Method used to free DNA from interior of the cell(s) or particle(s) |
| sc_lysis_method | Name of the kit or standard protocol used for cell(s) or particle(s) lysis |
| seq_meth | Sequencing machine used |
| seq_quality_check | Indicate if the sequence has been called by automatic systems (none) or under... |
| sim_search_meth | Tool used to compare ORFs with database, along with version and cutoffs used |
| sop | Standard operating procedures used in assembly and/or annotation of genomes, ... |
| sort_tech | Method used to sort/isolate cells or particles of interest |
| target_gene | Targeted gene or locus name for marker gene studies |
| target_subfragment | Name of subfragment of a gene or locus |
| tax_class | Method used for taxonomic classification, along with reference database used,... |
| tax_ident | The phylogenetic marker(s) used to assign an organism name to the SAG or MAG |
| trna_ext_software | Tools used for tRNA identification |
| trnas | The total number of tRNAs identified from the SAG or MAG |
| vir_ident_software | Tool(s) used for the identification of UViG as a viral genome, software or pr... |
| wga_amp_appr | Method used to amplify genomic DNA in preparation for sequencing |
| wga_amp_kit | Kit used to amplify genomic DNA in preparation for sequencing |
| x16s_recover | Can a 16S gene be recovered from the submitted SAG or MAG? |
| x16s_recover_software | Tools used for 16S rRNA gene extraction |